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- PDB-5yg3: Plasmodium vivax SHMT bound with PLP-glycine and S-GS834 -

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Basic information

Entry
Database: PDB / ID: 5yg3
TitlePlasmodium vivax SHMT bound with PLP-glycine and S-GS834
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE/INHIBITOR / alpha and beta protein / Transferase / methyltransferase activity / Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion
Similarity search - Function
: / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-8UC / Chem-PLG / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Model detailsPlasmodium vivax SHMT bound with PLP-glycine and GS834
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F.
CitationJournal: ChemMedChem / Year: 2018
Title: Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold
Authors: Schwertz, G. / Witschel, M.C. / Rottmann, M. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Amornwatcharapong, W. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Trapp, N. / Chaiyen, P. / Diederich, F.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,94111
Polymers147,7473
Non-polymers2,1948
Water4,306239
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9497
Polymers98,4982
Non-polymers1,4515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-56 kcal/mol
Surface area29860 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9858
Polymers98,4982
Non-polymers1,4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area9880 Å2
ΔGint-75 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.623, 58.727, 236.139
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-503-

CL

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 49249.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_140059500, PVP01_1453700, PVT01_140059000 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4H5I1, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical ChemComp-8UC / (3~{S})-6'-azanyl-7-fluoranyl-2,2,3'-trimethyl-5-pyridin-4-yl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5'-carbonitrile


Mass: 401.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H20FN5O
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→19.81 Å / Num. obs: 52746 / % possible obs: 96.1 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 14.8 / Num. measured all: 342285 / Scaling rejects: 371
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.473.80.38145970.9480.2110.43996.5
9.9-19.814.40.0515790.9980.0240.05770.2

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMR

4tmr


Resolution: 2.4→19.81 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / SU B: 13.486 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.897 / ESU R Free: 0.361
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3 5468 10.4 %RANDOM
Rwork0.2222 ---
obs0.2301 47271 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 102.02 Å2 / Biso mean: 38.325 Å2 / Biso min: 9.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å2-0.17 Å2
2--2.65 Å2-0 Å2
3----5.36 Å2
Refinement stepCycle: final / Resolution: 2.4→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 152 239 10765
Biso mean--40.93 29.64 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910725
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210341
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.97514511
X-RAY DIFFRACTIONr_angle_other_deg1.008323811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05825.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.748151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191548
X-RAY DIFFRACTIONr_chiral_restr0.0820.21608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022421
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 381 -
Rwork0.331 3551 -
all-3932 -
obs--95.81 %

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